Just noticed that in 1.4X, if you upgrade a core design the new design may disappaer from the Ship build list.
Using Yor Core ships. Colony Ship is one. I the Defender and Star Fury are others. Colony Ship has an Advanced Support module. If you delete or leave this module alone all works okay in upgrade. However, if you MOVE this module, you are charged the cost, get the benefit, and when you save the new design it does not appear in the Ship Builder window. I assume it has been tagged to appear when the required tech is availble.
Same thing happens with the Yor Defender - it has 2 phasor modules attached when it appears. And the Star Fury has a Railgun attached. Same thing happens if you move it.
It is confusing because these ships have modules equipped that are not active - i.e. the tech for them is not researched yet when they appear. Not sure if the advanced modules are there for 'bling' or some other reason - but something seems screwy.
Yes - I know, don't use Core Ships anyway - but I do use them as "Base Models" when in a hurry - I upgrade them, remove all the Active components, then add my own, then rename them - this time I noticed the behavior because I wanted to move one of the inactive modules out of the way and just put it somewhere else instead of deleting it.
Save game available that duplicates this behavior if needed.
Sorry if this has been reported already.